Variant report

Variant	rs4743196
Chromosome Location	chr9:101049252-101049253
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:101039245..101044695-chr9:101044948..101050216,8	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10118295	0.91[ASN][1000 genomes]
rs10120564	0.88[ASN][1000 genomes]
rs10739615	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10760233	0.93[ASN][1000 genomes]
rs10760243	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10818640	0.86[GIH][hapmap]
rs10818696	0.91[ASN][1000 genomes]
rs10818699	0.91[ASN][1000 genomes]
rs10818745	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs10985664	0.93[ASN][1000 genomes]
rs10985671	0.93[ASN][1000 genomes]
rs2117608	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4742723	0.93[ASN][1000 genomes]
rs4742724	0.93[ASN][1000 genomes]
rs4743187	0.86[GIH][hapmap]
rs4743195	0.93[ASN][1000 genomes]
rs55705027	0.88[ASN][1000 genomes]
rs58161463	0.82[EUR][1000 genomes]
rs59287552	0.93[ASN][1000 genomes]
rs60401554	0.88[ASN][1000 genomes]
rs62574279	0.88[ASN][1000 genomes]
rs62574292	0.93[ASN][1000 genomes]
rs7357704	0.83[EUR][1000 genomes]
rs748387	0.92[ASN][1000 genomes]
rs7847065	0.93[ASN][1000 genomes]
rs879368	0.86[GIH][hapmap]
rs9776328	0.88[ASN][1000 genomes]
rs995213	0.87[CEU][hapmap];0.82[GIH][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430085	chr9:100928245-101339645	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv831663	chr9:100941048-101109492	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1045780	chr9:100943318-101080389	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv540180	chr9:100943318-101080389	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv831664	chr9:101024862-101205637	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv519818	chr9:101024887-101092316	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4743196	TBC1D2	cis	Cerebellum	GTEx
rs4743196	TBC1D2	cis	Thyroid	GTEx
rs4743196	CORO2A	cis	Lymphoblastoid	GTEx
rs4743196	TBC1D2	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101037200-101051000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:101039800-101051000	Weak transcription	Fetal Intestine Small	intestine
3	chr9:101041400-101049400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:101043400-101051400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:101043600-101051000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr9:101049000-101062800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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